The normal vaginal microflora in healthy women of reproductive age plays a key role in preventing successful colonization by "undesirable" organisms including those responsible for bacterial vaginosis, yeast infections, sexually transmitted diseases and urinary tract infections. Our long-term goal is to develop an accurate understanding of the composition and ecology of the vagina microbial ecosystem in normal, healthy women as an essential prerequisite for comprehending how the normal microflora reduces the risk of acquiring these communicable diseases and for defining the factors determining disease susceptibility. The specific hypotheses are that 1. women's genetic backgrounds influence the composition of the vaginal microflora, 2. while vaginal community compositions markedly vary amongst women, the functional potential of a community is similar. Tools necessary to test these hypotheses will be developed and are addressed by these specific aims: 1. Conduct a comprehensive survey of the vaginal microflora in 400 women of different ethnic background using 16S rRNA gene sequencing analysis. We will correlate the community composition with genetic background, and provide the basis for Aim 2. 2. Develop a 16S rDNA-based molecular tool (molecular inversion probes) to rapidly and quantitatively measure the microbial species composition and abundance of a vaginal community. 3. Characterized the metabolic potential of the vaginal microflora of healthy women by community genomics. We will sequence the "community genome" of the five most predominant community types. Sequence data and analysis will be freely accessible through the web-based Vaginal Microbiome Database. 4. Develop the Vaginal Microbiome Expression GeneChip(c) array, a high density oligonucleotide microarray- based tool for functional genomic analyses of vaginal microbial communities. Using this tool we will assess community gene expression over the course of two months, while monitoring reproductive hormone levels. We view this work as analogous to the human genome project, in which initial sequence information provided a platform for decades of future work focused on all aspect of human health and disease. Similarly, these tools will be critical for the study and evaluation of women's health.